+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21893 | |||||||||
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Title | Cryo-EM structure of VASH1-SVBP bound to microtubules | |||||||||
Map data | Cryo-EM structure of VASH1-SVBP bound to microtubules | |||||||||
Sample |
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Keywords | Microtubule / Posttranslational modification / Detyrosination / Vasohibin / PROTEIN BINDING | |||||||||
Function / homology | Function and homology information regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / netrin receptor binding / Post-chaperonin tubulin folding pathway / axonemal microtubule / dorsal root ganglion development / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / regulation of cellular senescence ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / netrin receptor binding / Post-chaperonin tubulin folding pathway / axonemal microtubule / dorsal root ganglion development / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / negative regulation of lymphangiogenesis / organelle transport along microtubule / peptidase activator activity / glial cell differentiation / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / neuron projection arborization / cytoskeleton-dependent intracellular transport / cerebellar cortex morphogenesis / Formation of tubulin folding intermediates by CCT/TriC / dentate gyrus development / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / pyramidal neuron differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / Hedgehog 'off' state / Assembly and cell surface presentation of NMDA receptors / centrosome cycle / motor behavior / negative regulation of endothelial cell migration / COPI-dependent Golgi-to-ER retrograde traffic / labyrinthine layer blood vessel development / response to L-glutamate / smoothened signaling pathway / intercellular bridge / regulation of synapse organization / axon development / startle response / negative regulation of endothelial cell proliferation / locomotory exploration behavior / Recycling pathway of L1 / microtubule polymerization / microtubule-based process / negative regulation of blood vessel endothelial cell migration / protein secretion / RHO GTPases activate IQGAPs / response to tumor necrosis factor / regulation of angiogenesis / response to mechanical stimulus / COPI-mediated anterograde transport / metallocarboxypeptidase activity / Activation of AMPK downstream of NMDARs / condensed chromosome / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / homeostasis of number of cells within a tissue / negative regulation of protein ubiquitination / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / cellular response to calcium ion / AURKA Activation by TPX2 / negative regulation of angiogenesis / adult locomotory behavior / filopodium / axon guidance / cell periphery / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / RHO GTPases Activate Formins / peptide binding / neuron migration / synapse organization / visual learning / neuromuscular junction / PKR-mediated signaling / recycling endosome / cerebral cortex development / mitotic spindle / structural constituent of cytoskeleton / memory / microtubule cytoskeleton organization / response to wounding / Aggrephagy / HCMV Early Events / cytoplasmic ribonucleoprotein granule / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / lamellipodium Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Li F / Li Y | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Elife / Year: 2020 Title: Cryo-EM structure of VASH1-SVBP bound to microtubules. Authors: Faxiang Li / Yang Li / Xuecheng Ye / Haishan Gao / Zhubing Shi / Xuelian Luo / Luke M Rice / Hongtao Yu / Abstract: The dynamic tyrosination-detyrosination cycle of α-tubulin regulates microtubule functions. Perturbation of this cycle impairs mitosis, neural physiology, and cardiomyocyte contraction. The ...The dynamic tyrosination-detyrosination cycle of α-tubulin regulates microtubule functions. Perturbation of this cycle impairs mitosis, neural physiology, and cardiomyocyte contraction. The carboxypeptidases vasohibins 1 and 2 (VASH1 and VASH2), in complex with the small vasohibin-binding protein (SVBP), mediate α-tubulin detyrosination. These enzymes detyrosinate microtubules more efficiently than soluble αβ-tubulin heterodimers. The structural basis for this substrate preference is not understood. Using cryo-electron microscopy (cryo-EM), we have determined the structure of human VASH1-SVBP bound to microtubules. The acidic C-terminal tail of α-tubulin binds to a positively charged groove near the active site of VASH1. VASH1 forms multiple additional contacts with the globular domain of α-tubulin, including contacts with a second α-tubulin in an adjacent protofilament. Simultaneous engagement of two protofilaments by VASH1 can only occur within the microtubule lattice, but not with free αβ heterodimers. These lattice-specific interactions enable preferential detyrosination of microtubules by VASH1. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21893.map.gz | 95.1 MB | EMDB map data format | |
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Header (meta data) | emd-21893-v30.xml emd-21893.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_21893.png | 118 KB | ||
Filedesc metadata | emd-21893.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21893 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21893 | HTTPS FTP |
-Validation report
Summary document | emd_21893_validation.pdf.gz | 529.9 KB | Display | EMDB validaton report |
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Full document | emd_21893_full_validation.pdf.gz | 529.5 KB | Display | |
Data in XML | emd_21893_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | emd_21893_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21893 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21893 | HTTPS FTP |
-Related structure data
Related structure data | 6wslMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21893.map.gz / Format: CCP4 / Size: 101.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of VASH1-SVBP bound to microtubules | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Tenary complex of microtubule with VASH1-SVBP complex
Entire | Name: Tenary complex of microtubule with VASH1-SVBP complex |
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Components |
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-Supramolecule #1: Tenary complex of microtubule with VASH1-SVBP complex
Supramolecule | Name: Tenary complex of microtubule with VASH1-SVBP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Tubulin alpha-1A chain
Macromolecule | Name: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50.188441 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY UniProtKB: Tubulin alpha-1A chain |
-Macromolecule #2: Tubulin beta-3 chain
Macromolecule | Name: Tubulin beta-3 chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50.48152 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPSGNYVGDS DLQLERISVY YNEASSHKYV PRAILVDLEP GTMDSVRSGA FGHLFRPDN FIFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKECENCDC LQGFQLTHSL GGGTGSGMGT LLISKVREEY P DRIMNTFS ...String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPSGNYVGDS DLQLERISVY YNEASSHKYV PRAILVDLEP GTMDSVRSGA FGHLFRPDN FIFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKECENCDC LQGFQLTHSL GGGTGSGMGT LLISKVREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS IHQLVENTDE TYCIDNEALY DICFRTLKLA TPTYGDLNHL VSATMSGVTT SL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTARG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVATVF RGR MSMKEV DEQMLAIQSK NSSYFVEWIP NNVKVAVCDI PPRGLKMSST FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEGE MYEDDEEESE AQGPK UniProtKB: Tubulin beta-3 chain |
-Macromolecule #3: Tubulinyl-Tyr carboxypeptidase 1
Macromolecule | Name: Tubulinyl-Tyr carboxypeptidase 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: tubulinyl-Tyr carboxypeptidase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 29.780445 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: DLRDGGVPFF VNRGGLPVDE ATWERMWKHV AKIHPDGEKV AQRIRGATDL PKIPIPSVPT FQPSTPVPER LEAVQRYIRE LQYNHTGTQ FFEIKKSRPL TGLMDLAKEM TKEALPIKCL EAVILGIYLT NSMPTLERFP ISFKTYFSGN YFRHIVLGVN F AGRYGALG ...String: DLRDGGVPFF VNRGGLPVDE ATWERMWKHV AKIHPDGEKV AQRIRGATDL PKIPIPSVPT FQPSTPVPER LEAVQRYIRE LQYNHTGTQ FFEIKKSRPL TGLMDLAKEM TKEALPIKCL EAVILGIYLT NSMPTLERFP ISFKTYFSGN YFRHIVLGVN F AGRYGALG MSRREDLMYK PPAFRTLSEL VLDFEAAYGR CWHVLKKVKL GQSVSHDPHS VEQIEWKHSV LDVERLGRDD FR KELERHA RDMRLKIGKG TG UniProtKB: Tubulinyl-Tyr carboxypeptidase 1 |
-Macromolecule #4: Small vasohibin-binding protein
Macromolecule | Name: Small vasohibin-binding protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 7.821939 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MDPPARKEKT KVKESVSRVE KAKQKSAQQE LKQRQRAEIY ALNRVMTELE QQQFDEFCKQ MQPPGE UniProtKB: Small vasohibin-binding protein |
-Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #6: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Macromolecule | Name: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: G2P |
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Molecular weight | Theoretical: 521.208 Da |
Chemical component information | ChemComp-G2P: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 86 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46999 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |